Sequence
atgc intronic sequence ATGC exonic sequencegtttgtttatctaagcctcattgatttttgactcttaaaagaaccaggtgttcattgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G66470.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g49220.2 (Oryza sativa), 3'ss of exon 2
-------gtttgtttatctaagcctcattgatttttgactcttaaaagaaccaggtgttcattgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
||| | ||||| || |||| | |||| | ||| | | |||| ||| || || || | | || | || | | |||||||| ||||||||||| ||||| ||||| || | ||| | ||||| | | |||| |||||||||||||||||||| || ||| | || |
gtatcaccttttagtttctaaagctttaggattatagactatgaaaggggg-aaatgttaatttctca--ctgcta----atctgagttatcatttagT-----------TTGCAGATAATACTTTATGACACGCCAGGTGTCATCAAAAAGGAAATGCATAAGCTAGACACAATGATGATGAAGAATGTTAGGAGTGCCGTTGGCAGT-------
upper sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os05g49220.1 (Oryza sativa), 3'ss of exon 2
-------gtttgtttatctaagcctcattgatttttgactcttaaaagaaccaggtgttcattgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
||| | ||||| || |||| | |||| | ||| | | |||| ||| || || || | | || | || | | |||||||| ||||||||||| ||||| ||||| || | ||| | ||||| | | |||| |||||||||||||||||||| || ||| | || ||| || |
gtatcaccttttagtttctaaagctttaggattatagactatgaaaggggg-aaatgttaatttctca--ctgcta----atctgagttatcatttagt-----------ttgcagATAATACTTTATGACACGCCAGGTGTCATCAAAAAGGAAATGCATAAGCTAGACACAATGATGATGAAGAATGTTAGGAGTGCCGTTGGCAGTGCAGATT
upper sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA02G06100.1 (Glycine max), 3'ss of exon 2
gtttgtttatctaagcctcattgatttttgactcttaaaagaacca-ggtgttcattgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
| ||| || | | | | | | | | | || | | || || | ||| ||| ||| | |||| | | | | |||||||||||||||||||| | ||||||||| | ||||| | ||||| | |||||| ||||||||||||| ||||| | ||| || | ||||| ||||
----aaaattttaatactgaattttactaaattaatggatgtacaatagaatttatatttatattttttatttt--ttatttttctgacttttgaa----tctcttgcagATGATACTTTATGACAAACCTGGTGTACTACAGAAGGAAATGCATAAGTTAGACTCAATGATGATGAAAAATGTTCGCAGTGCGGCAGTTAATGCTGACT
upper sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G24870.1 (Glycine max), 3'ss of exon 2
gtttgtttatctaagcctcattgatttttgactcttaaaagaaccaggtgttcattgcttggtttgatatagaaattaagatgt--cgactgatacaa--gcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
|| | | || | | | | | | ||| | | || || |||| || | ||| | | | |||||| | | | |||||||||||||||||||| || |||||||| | ||||| | |||||| |||||| ||||||||||||| || || | |||||| | ||||| ||||
-----------aaaacaactttaagtact--ttttcagttgaataaaattttaatactgaattttgctaaattaatggatgtacaacagATGATACTTTTGAATCTCTTGCAGATGATACTTTATGACACACCTGGTGTTCTACAGAAGGAAATGCACTTGTTAGACTCAATGATGATGAAAAACGTTCGCAGTGCTGCAGTTAATGCTGACT
upper sequence: AT5G66470.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv04s0023g02120.t01 (Vitis vinifera), 3'ss of exon 2
gtttgtttatctaagcctcattgatttttgactcttaaaagaaccaggtgttcattgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
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----aaatacataaacat-acacaaccccatgccttcacacacacatataaaagtaatatgctat----taagctcttaaaaacgcatgaacttatgttttgcttgtagATGATACTTTATGACACACCTGGTGTTATTGAGAAGAAAATGCACAAGTTGGACTCCATGATGATGAAGAATGTCCGCAGTGCTACCATTAATGCGGACTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124890339|gb|EH969241.1|EH969241EST: AAACGACGAGGCATCGGATTCTTGGTATTTGTTCTAGCCCTGAATATCAG ATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAG
genomic: AAACGACGAGGCATCGGATTCTTGGTATTTGTTCTAGCCCTGAATATCAGgtttgtttat ... tgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
gactgat putative branch site (score: 3)
tttgatatagaaatta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtttatctaagcctcattgatttttgactcttaaaagaaccaggtgttcattgcttggtttgatatagaaattaagatgtcgactgatacaagcttgtgttgcagATGATACTTTATGATACGCCTGGTGTAATTGAGAAGAAGATGCACAGGTTAGATACAATGATGATGAAGAATGTCAGAGATGCTGCCATCAATGCGGACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC